| line |
!l |
l&&!r |
l&&r |
condition |
|
163
|
0 |
4 |
6 |
$u_name and defined $Bio::Map::Gene::GENES->{$u_name} |
|
351
|
0 |
0 |
320 |
$map and $self->in_map($map) |
|
381
|
0 |
0 |
2 |
$pos and $pos->isa('Bio::Map::GenePosition') |
|
438
|
0 |
0 |
3 |
$int > 0 and $int <= @transcripts |
|
499
|
95 |
0 |
4 |
@transcripts == 0 and $value == 0 |
|
617
|
11 |
0 |
9 |
@exons == 0 and $exon_num == 1 |
|
755
|
0 |
0 |
0 |
$trans_ref and @{$trans_ref;} > 0 |
|
857
|
276 |
4 |
37 |
defined $transcript_number and $transcript_number == 0 |
|
909
|
0 |
0 |
110 |
$wanted and $wanted > 0 |
|
912
|
0 |
1 |
107 |
$index >= 0 and $index <= $#list |
|
921
|
0 |
0 |
6 |
$pos and $pos->isa('Bio::Map::GenePosition') |
|
930
|
0 |
0 |
0 |
$self->warn('no transcript pos end for pos for gene ' . $self->universal_name . ' and species ' . $pos->map->species . '!') and exit |
|
931
|
0 |
0 |
0 |
$self->warn('no pos end for pos for gene ' . $self->universal_name . ' and species ' . $pos->map->species . '!') and exit |
|
947
|
1 |
0 |
0 |
ref $thing and $thing->isa('Bio::Map::GeneMap') |
|
951
|
1 |
0 |
0 |
$map and $map->isa('Bio::Map::GeneMap') |
| line |
l |
!l |
condition |
|
536
|
0 |
12 |
$transcript_num ||= 0 |
|
541
|
2 |
0 |
$thing->map || (return) |
|
592
|
3 |
19 |
$value ||= 0 |
|
660
|
1 |
4 |
$value ||= 0 |
|
732
|
9 |
0 |
$self->universal_name || (return 0) |
|
737
|
0 |
0 |
'Bio::Tools::Run::Ensembl'->get_adaptor($species, 'Slice') || (return 0) |
|
738
|
0 |
0 |
'Bio::Tools::Run::Ensembl'->get_gene_by_name('-species', $species, '-name', $gene_name, '-use_orthologues', 'Homo sapiens', '-use_swiss_lookup', 1, '-use_entrez_lookup', 1) || (return 0) |
|
867
|
41 |
0 |
$pos->relative || (next) |
|
945
|
1 |
0 |
$self->{$type}{'general'} || '' |
|
948
|
0 |
0 |
$self->{$type}{$thing} || '' |
|
964
|
7 |
0 |
$map->unique_id || (return) |
| line |
l |
!l&&r |
!l&&!r |
condition |
|
383
|
2 |
0 |
0 |
$pos->map || $self->throw('Supplied GenePosition has no map') |
|
497
|
9 |
86 |
4 |
$value ||= $self->active_transcript($map) |
|
552
|
11 |
1 |
0 |
$pos || $self->get_transcript_position($thing, $transcript_num) |
|
733
|
0 |
0 |
9 |
$SET_FROM_DB or $self->{'_set_from_db'} |
|
869
|
0 |
41 |
0 |
$rel->transcript || $self->active_transcript($map) |
|
923
|
6 |
0 |
0 |
$pos->map || $self->throw('Supplied GenePosition has no map') |
|
926
|
2 |
0 |
0 |
$self->active_transcript($map) || $self->throw('Asked to be relative to the active transcript, but there is no transcript') |
|
|
4 |
2 |
0 |
$transcript_num ||= $self->active_transcript($map) || $self->throw('Asked to be relative to the active transcript, but there is no transcript') |
|
929
|
6 |
0 |
0 |
$self->get_transcript_position($map, $transcript_num) || $self->throw("Asked to be relative to transcript $transcript_num, but there is no such transcript") |